They could be just cutting Negi some slack because he's still a kid. That, and I believe that everyone of his students has some sort of connection to the magical world that they themselves are unaware of. (exp. Konoka, Misora, and Yuuna)
I'm saying that those in his class that don't know of the magical world might have a connection to it. (exp. Yuuna) And its a hunch, I have that Akamatsu-sensei will later reveal that all or some of the girls in 3-A will have some sort of connection in one way or another.
From what I read in the Wikipedia article on Negima, Fate attacks Negi, and injures him badly. Fate is apparently the main antagonist of Negima. I need more information on Fate attacking Negi.